************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 fgf13.phase.inp fgf13.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST fgf13.phase.out_freqs : haplotype frequency estimates fgf13.phase.out_pairs : most likely haplotype pairs for each individual fgf13.phase.out_recom : estimates of recombination parameters fgf13.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 14 Positions of loci: 531 647 2736 5904 11346 26538 56383 57071 57128 67035 78418 82334 82444 82619 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file fgf13.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCCAAACGGTCDDA 25.000000 2 GCCATACGGTCDDA 5.000000 3 GTCAAACGGTCDDA 9.000000 4 GTCAAGCAGTCDDA 5.000000 5 GTCAAGCAGCTDIG 14.000000 6 GTCAAGTATTCDDA 12.000000 7 GTCATACGGTCDDA 15.000000 8 GTCATGCGGTCDDA 1.000000 9 GTCATGTATTCDDA 29.000000 10 GTTAAGCAGTCDDA 3.000000 11 GTTGAGCAGTCDDA 3.000000 12 GTTGAGCAGCTDIG 3.000000 13 GTTGTGCAGTCDDA 5.000000 14 CTCAAACGGTCDDA 7.000000 15 CTCATACGGTCDDA 31.000000 16 CTCATACGGTCIDA 10.000000 17 CTCATGCGGCCDIG 2.000000 18 CTCATGTATTCDDA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,7) P002: (5,7) P003: (7,7) P004: (9,10) P005: (5,7) P006: (1,1) P007: (14,14) P008: (1,15) P009: (1,16) P010: (1,9) P011: (9,9) P012: (15,15) P013: (6,15) P014: (5,18) P015: (15,15) P016: (5,5) P017: (1,7) P018: (12,12) P019: (16,16) P020: (1,17) P021: (11,11) P022: (1,1) P023: (6,16) P024: (9,9) P025: (9,9) P026: (5,9) P027: (3,9) P028: (15,16) P029: (10,10) P030: (14,14) P031: (16,16) P032: (4,13) P033: (1,4) P034: (6,15) P035: (6,6) P036: (9,9) P037: (3,3) P038: (4,9) P039: (6,14) P040: (14,14) P041: (9,9) P042: (9,9) P043: (3,15) P044: (3,3) P045: (9,9) P046: (15,15) P047: (5,5) P048: (1,8) P049: (1,11) P050: (9,9) P051: (15,15) P052: (7,15) P053: (9,9) P054: (15,15) P055: (7,7) P056: (5,5) P057: (1,1) P058: (15,15) P059: (9,9) P060: (5,5) P061: (13,13) P062: (2,2) P063: (1,1) P064: (6,12) P065: (9,9) P066: (7,7) P067: (1,6) P068: (6,6) P069: (1,7) P070: (1,1) P071: (1,1) P072: (1,15) P073: (15,15) P074: (13,13) P075: (5,5) P076: (7,17) P077: (15,15) P078: (7,16) P079: (6,16) P080: (1,9) P081: (15,15) P082: (3,15) P083: (15,15) P084: (2,9) P085: (2,2) P086: (15,15) P087: (3,7) P088: (4,4) P089: (3,6) P090: (15,16) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 G (C) C A A A C G G T C D D A G (T) C A T A C G G T C D D A 0 P002 G T C A A G C A G C T D I G G T C A T A C G G T C D D A 0 P003 G T C A T A C G G T C D D A G T C A T A C G G T C D D A 0 P004 G T C A T G T A T T C D D A G T T A A G C A G T C D D A 0 P005 G T C A A G C A G C T D I G G T C A T A C G G T C D D A 0 P006 G C C A A A C G G T C D D A G C C A A A C G G T C D D A 0 P007 C T C A A A C G G T C D D A C T C A A A C G G T C D D A 0 P008 G C C A A A C G G T C D D A C T C A T A C G G T C D D A 0 P009 G C C A A A C G G T C D D A C T C A T A C G G T C I D A 0 P010 G C C A A A C G G T C D D A G T C A T G T A T T C D D A 0 P011 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P012 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P013 G T C A (A) G T A T T C D D A C T C A (T) A C G G T C D D A 0 P014 (G) T C A A G C A G C T D I G (C) T C A T G T A T T C D D A 0 P015 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P016 G T C A A G C A G C T D I G G T C A A G C A G C T D I G 0 P017 G (C) C A A A C G G T C D D A G (T) C A T A C G G T C D D A 0 P018 G T T G A G C A G C T D I G G T T G A G C A G C T D I G 0 P019 C T C A T A C G G T C I D A C T C A T A C G G T C I D A 0 P020 G C C A A A C G G T C D D A C T C A T G C G G C C D I G 0 P021 G T T G A G C A G T C D D A G T T G A G C A G T C D D A 0 P022 G C C A A A C G G T C D D A G C C A A A C G G T C D D A 0 P023 G T C A A G T A T T C D D A C T C A T A C G G T C I D A 0 P024 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P025 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P026 G T C A A G C A G C T D I G G T C A T G T A T T C D D A 0 P027 G T C A (A) A C G G T C D D A G T C A (T) G T A T T C D D A 0 P028 C T C A T A C G G T C D D A C T C A T A C G G T C I D A 0 P029 G T T A A G C A G T C D D A G T T A A G C A G T C D D A 0 P030 C T C A A A C G G T C D D A C T C A A A C G G T C D D A 0 P031 C T C A T A C G G T C I D A C T C A T A C G G T C I D A 0 P032 G T C A A G C A G T C D D A G T T G T G C A G T C D D A 0 P033 G C C A A A C G G T C D D A G T C A A G C A G T C D D A 0 P034 G T C A (A) G T A T T C D D A C T C A (T) A C G G T C D D A 0 P035 G T C A A G T A T T C D D A G T C A A G T A T T C D D A 0 P036 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P037 G T C A A A C G G T C D D A G T C A A A C G G T C D D A 0 P038 G T C A A G C A G T C D D A G T C A T G T A T T C D D A 0 P039 G T C A A G T A T T C D D A C T C A A A C G G T C D D A 0 P040 C T C A A A C G G T C D D A C T C A A A C G G T C D D A 0 P041 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P042 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P043 (G) T C A A A C G G T C D D A (C) T C A T A C G G T C D D A 0 P044 G T C A A A C G G T C D D A G T C A A A C G G T C D D A 0 P045 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P046 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P047 G T C A A G C A G C T D I G G T C A A G C A G C T D I G 0 P048 G C C A (A) (A) C G G T C D D A G T C A (T) (G) C G G T C D D A 0 P049 G C C A A A C G G T C D D A G T T G A G C A G T C D D A 0 P050 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P051 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P052 G T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P053 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P054 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P055 G T C A T A C G G T C D D A G T C A T A C G G T C D D A 0 P056 G T C A A G C A G C T D I G G T C A A G C A G C T D I G 0 P057 G [C] C A A A C G G T C D D A G C C A A A C G G T C D D A 0 P058 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P059 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P060 G T C A A G C A G C T D I G G T C A A G C A G C T D I G 0 P061 G T T G T G C A G T C D D A G T T G T G C A G T C D D A 0 P062 G C C A T A C G G T C D D A G C C A T A C G G T C D D A 0 P063 G C C A A A C G G T C D D A G C C A A A C G G T C D D A 0 P064 G T C A A G T A T T C D D A G T T G A G C A G C T D I G 0 P065 G T C A T G T A T T C D D A G T C A T G T A T T C D D A 0 P066 G T C A T A C G G T C D D A G T C A T A C G G T C D D A 0 P067 G C C A A A C G G T C D D A G T C A A G T A T T C D D A 0 P068 G T C A A G T A T T C D D A G T C A A G T A T T C D D A 0 P069 G (C) C A A A C G G T C D D A G (T) C A T A C G G T C D D A 0 P070 G C C A A A C G G T C D D A G C C A A A C G G T C D D A 0 P071 G C C A A A C G G T C D D A G C C A A A C G G T C D D A 0 P072 G C C A A A C G G T C D D A C T C A T A C G G T C D D A 0 P073 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P074 G T T G T G C A G T C D D A G T T G T G C A G T C D D A 0 P075 G T C A A G C A G C T D I G G T C A A G C A G C T D I G 0 P076 G T C A T A C G G T C D D A C T C A T G C G G C C D I G 0 P077 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P078 G T C A T A C G G T C D D A C T C A T A C G G T C I D A 0 P079 G T C A A G T A T T C D D A [C] T C A T A C G G T C I D A 0 P080 G C C A A A C G G T C D D A G T C A T G T A T T C D D A 0 P081 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P082 (G) T C A A A C G G T C D D A (C) T C A T A C G G T C D D A 0 P083 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P084 G C C A T A C G G T C D D A G T C A T G T A T T C D D A 0 P085 G C C A T A C G G T C D D A G C C A T A C G G T C D D A 0 P086 C T C A T A C G G T C D D A C T C A T A C G G T C D D A 0 P087 G T C A A A C G G T C D D A G T C A T A C G G T C D D A 0 P088 G T C A A G C A G T C D D A G T C A A G C A G T C D D A 0 P089 G T C A A A C G G T C D D A G T C A A G [T] A [T] T C D D A 0 P090 C T C A T A C G G T C D D A C T C A T A C G G T C I D A END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 P001 = (C) = = A = = ? ? = = = = = = (T) = = T = = ? ? = = = = = 0 P002 = = = = A G = A ? C T = I G = = = = T A = G ? T C = D A 0 P003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P004 = = C = T = T = T = = = = = = = T = A = C = G = = = = = 0 P005 = = = = A G = A = C T = I G = = = = T A = G = T C = D A 0 P006 = = = ? = = = = = = = = = = = = = ? = = = = = = = = = = 0 P007 = = = = = = = = ? = = = = = = = = = = = = = ? = = = = = 0 P008 G C ? = A = = = = = = = = = C T ? = T = = = = = = = = = 0 P009 G C = = A = ? ? ? = = D = = C T = = T = ? ? ? = = I = = 0 P010 = C = = A A C G G = = = = = = T = = T G T A T = = = = = 0 P011 = = = = = = = ? ? = = = = = = = = = = = = ? ? = = = = = 0 P012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P013 G = = = (A) G T A ? = = = = = C = = = (T) A C G ? = = = = = 0 P014 (G) = = = A = C = G C T = I ? (C) = = = T = T = T T C = D ? 0 P015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P016 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P017 = (C) = = A = = = = = = = = = = (T) = = T = = = = = = = = = 0 P018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P019 = = = = = = = ? ? = = = = = = = = = = = = ? ? = = = = = 0 P020 G C = = A A = = = ? = = D A C T = = T G = = = ? = = I G 0 P021 = = = = = = = = = = = = = ? = = = = = = = = = = = = = ? 0 P022 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P023 G = = = A G T A T = = D = = C = = = T A C G G = = I = = 0 P024 = = = = = = ? = = = = = = = = = = = = = ? = = = = = = = 0 P025 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P026 = = = = A = C = G C T = I G = = = = T = T = T T C = D A 0 P027 = = = = (A) A C G G = = = = = = = = = (T) G T A T = = = = = 0 P028 = = = = = = = = = = = D = = = = = = = = = = = = = I = = 0 P029 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P030 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P031 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P032 = = C A A = = = = = = = = = = = T G T = = = = = = = = = 0 P033 = C = = = A = G = = = = = = = T = = = G = A = = = = = = 0 P034 G = = = (A) G T A T = = = = = C = = = (T) A C G G = = = = = 0 P035 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P036 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P037 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P038 = = = = A = C = G = = = = = = = = = T = T = T = = = = = 0 P039 G = = = = G T A T = = = = = C = = = = A C G G = = = = = 0 P040 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P041 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P042 = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = 0 P043 (G) = = = A = = = = = = = = = (C) = = = T = = = = = = = = = 0 P044 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P045 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P046 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P047 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P048 = C = = (A) (A) = = = = = = = = = T = = (T) (G) = = = = = = = = 0 P049 = C C A = A = G = = = = = = = T T G = G = A = = = = = = 0 P050 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P051 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P052 G = = = = = = = = = = = = = C = = = = = = = = = = = = = 0 P053 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P054 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P055 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P056 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P057 = ? = = = = = ? ? = = = = ? = ? = = = = = ? ? = = = = ? 0 P058 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P059 = = = = = = = = = = = = = ? = = = = = = = = = = = = = ? 0 P060 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P061 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P062 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P063 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P064 = = C A = = T = T T C = D A = = T G = = C = G C T = I G 0 P065 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P066 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P067 = C = = = A C G G = = = = = = T = = = G T A T = = = = = 0 P068 = = = ? = = = ? ? = = = = = = = = ? = = = ? ? = = = = = 0 P069 = (C) = = A = = = = = = = = = = (T) = = T = = = = = = = = = 0 P070 = = = = = = = ? ? = = = = ? = = = = = = = ? ? = = = = ? 0 P071 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P072 G C = = A = = = = = = = = = C T = = T = = = = = = = = = 0 P073 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P074 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P075 = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = 0 P076 G = = = = A = = = T = = D A C = = = = G = = = C = = I G 0 P077 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P078 G = = = = = = = = = = D = = C = = = = = = = = = = I = = 0 P079 ? ? = = A G T A T = = D = = ? ? = = T A C G G = = I = = 0 P080 = C = = A A C G G = = = = = = T = = T G T A T = = = = = 0 P081 = = = = = = ? ? ? = = = = = = = = = = = ? ? ? = = = = = 0 P082 (G) = = = A = = = ? = = = = = (C) = = = T = = = ? = = = = = 0 P083 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P084 = C = = = A C G G = = = = = = T = = = G T A T = = = = = 0 P085 = = = = = = = ? ? = = = = = = = = = = = = ? ? = = = = = 0 P086 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P087 = = = = A = = = = = = = = = = = = = T = = = = = = = = = 0 P088 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P089 = = = = = A ? ? ? ? = = = = = = = = = G ? ? ? ? = = = = 0 P090 = = = = = = ? ? ? = = D = = = = = = = = ? ? ? = = I = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = 0.85 = = 1.00 = = ? ? = = = = = = = = = 0.99 1.00 = 1.00 ? 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 = 1.00 = = = = = = = = = 0.99 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = 1.00 1.00 ? = 0.92 = = = = = = = = = 1.00 1.00 = = 1.00 = ? ? ? = = 0.98 = = = 1.00 = = 0.90 1.00 1.00 1.00 1.00 = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = 0.98 = = = 0.55 1.00 1.00 1.00 ? = = = = = 0.54 = = = 0.92 = 1.00 = 1.00 1.00 1.00 = 1.00 ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.85 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = 0.98 0.98 = = 0.99 1.00 = = = ? = = 1.00 1.00 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = 1.00 = = = 0.97 1.00 1.00 1.00 1.00 = = 0.97 = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = 0.60 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 0.98 = = = = = = = = = = 0.99 = = = 1.00 = 1.00 = = = = = = 0.98 = = = 0.55 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = 1.00 = 1.00 = = = = = 0.98 = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = 0.66 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.98 = = 0.81 0.88 = = = = = = = = = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = = = = = ? = = = ? ? = = = = = = 0.85 = = 1.00 = = = = = = = = = = = = = = = = ? ? = = = = ? = = = = = = = = = = = = = = 1.00 1.00 = = 0.92 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = 0.95 = = = = 1.00 = = = 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = 0.95 = = = = = = = = = = 1.00 = = ? ? = = 0.90 1.00 1.00 1.00 1.00 = = 0.95 = = = 1.00 = = 0.90 1.00 1.00 1.00 1.00 = = = = = = = = = = = ? ? ? = = = = = 0.66 = = = 1.00 = = = ? = = = = = = = = = = = = = = = = = = = = 0.98 = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 ? ? ? ? = = = = = = = = = = ? ? ? = = 1.00 = = END PHASEPROBS